From owner-chemistry#* at *#ccl.net Fri Nov  4 13:50:01 2005
From: "TJ O Donnell tjo:-:acm.org" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: Dipole Moments and Molecular Fragments
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X-Original-From: "TJ O'Donnell" <tjo]![acm.org>
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Date: Fri, 04 Nov 2005 10:23:01 -0800
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Sent to CCL by: "TJ O'Donnell" [tjo.^^.acm.org]
I agree, in particular:
 > I think chemists have attached too much
 > significance to the undeniable separation of charge that exists between
 > bonded atoms of different electronegativities, mainly because there was
 > no way to demonstrate that these charge separations were not necessarily
 > quantitatively or qualitatively different from any others that might be
 > defined for the system.

There are many molecular properties that are successfully computed using
fragments, whether they be atom fragments, bond fragments or group fragments -
clogp, heats of formation, dipole moments, etc.
The choice of fragments is arbitrary and similar results can be obtained using other
fragments.  For example, clogp is famously computed using group fragments,
such as those defined by Al Leo, et. al.  But it can be computed just as well
(IMHO) using atom fragments.  One can argue statistics about the fit to clogp
for one method compared to the other, but the results of such arguments only
lead to a decision about which method is more predictive/useful, not which method is
more correct nor which more accurately represents some underlying physics.

Any molecular property is truly a property unique to that particular molecule
and (never?) uniquely attributable to any sums of fragments.  Fragment analyses
are always arbitrary, albeit superbly practical and useful.

One exception might be molecular weight, which is uniquely attributable to a sum
of atomic weights.  But this might be considered more of a definition and it surely
DOES reveal something about the underlying physics.  It arises from the fact/observation
that the nuclear mass of one atom is unaffected by that of neighboring atoms.
Electrons don't behave like that, as we all know.
Otherwise chemistry would be simply physics.

TJ O'Donnell
gNova Scientific Software
http://www.gnova.com/

Phil Hultin hultin.:.cc.umanitoba.ca wrote:
> The question about dipole moments of charged species is related to 
> another issue, which is somewhat of a hobby-horse of mine.
> 
>  
> 
> In organic chemistry and biochemistry particularly, structural and 
> mechanistic rationales are often based on the idea of “fragment dipoles” 
> and their interactions with one another.  In small molecules these are 
> usually dipoles said to be associated with polar covalent bonds, while 
> in proteins the so-called helix dipole is another example.
> 
>  
> 
> For many years I accepted the idea that “intramolecular dipole-dipole 
> repulsions” were good explanations for all kinds of phenomena, but I am 
> in serious doubt about that idea now.  When you start to dissect the 
> overall dipole moment of a molecule, you enter into the same kind of 
> origin-dependence that you see in ions.  What makes the arbitrary choice 
> of a bond dipole or a helix dipole more significant than the infinitude 
> of other point-to-point dipoles that could be defined within the 
> molecular charge envelope?  I think chemists have attached too much 
> significance to the undeniable separation of charge that exists between 
> bonded atoms of different electronegativities, mainly because there was 
> no way to demonstrate that these charge separations were not necessarily 
> quantitatively or qualitatively different from any others that might be 
> defined for the system.
> 
>  
> 
> We have looked at charge distributions to seek evidence for fragment 
> dipoles and their interactions, and we haven’t seen anything convincing. 
>  Do others have any opinions on this?
> 
>  
> 
> Dr. Philip G. Hultin
> 
> Associate Professor of Chemistry,
> 
> University of Manitoba
> 
> Winnipeg, MB
> 
> R3T 2N2
> 
> hultin]^[cc.umanitoba.ca <mailto:hultin]^[cc.umanitoba.ca>
> 
> http://umanitoba.ca/chemistry/people/hultin
> 
>  
>